MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands.
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands.
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MobilomeFINDER：基于网络的工具，用于计算机和实验发现细菌基因组岛。
DOI：
10.1093/nar/gkm380
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发表时间：
2007-07
影响因子：
14.9
通讯作者：
Rajakumar K
中科院分区：
文献类型：
--
作者：
Ou HY;He X;Harrison EM;Kulasekara BR;Thani AB;Kadioglu A;Lory S;Hinton JC;Barer MR;Deng Z;Rajakumar K
MobilomeFINDER（http：//mml.sjtu.edu.cn/MobilomeFINDER）是一个互动的在线工具，它有助于细菌基因组岛或“移动的基因组”（mobilome）的发现;它集成了ArrayOme和tRNAcc软件包。ArrayOme利用微阵列衍生的比较基因组杂交输入数据集来生成通过合并被分类为“存在”的相邻基因而产生的“推断的重叠群”。这些“片段”共同代表一个假设的“微阵列可视化基因组（MVG基因组）”。ArrayOme允许识别物理基因组和MVG大小之间的不一致性，从而能够鉴定富含微阵列难以捉摸的新基因的菌株。单个tRNAcc工具通过比较分析密切相关的测序基因组中tRNA位点和其他整合热点的内容和背景，促进了基因组岛的自动识别。辅助工具有助于设计热点侧翼引物，用于对未测序菌株中的同源基因座进行计算机模拟和/或基于湿科学的询问，并分析岛屿的特征，以提示外源来源;将岛屿特异性和基因组背景特征制成表格，并以示意图和图形形式表示。到目前为止，我们已经使用MobilomeFinder分析了几种肠杆菌科，铜绿假单胞菌和猪链球菌的基因组。MobilomeFINDER通过增加对新出现的序列数据的利用和对未测序的测试菌株进行基于PCR的分析，实现了高通量岛的鉴定和表征;随后基于靶向酵母重组的捕获允许对新基因组岛进行全长测序和详细的功能研究。
MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or ‘mobile genome’ (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate ‘inferred contigs’ produced by merging adjacent genes classified as ‘present’. Collectively these ‘fragments’ represent a hypothetical ‘microarray-visualized genome (MVG)’. ArrayOme permits recognition of discordances between physical genome and MVG sizes, thereby enabling identification of strains rich in microarray-elusive novel genes. Individual tRNAcc tools facilitate automated identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites and other integration hotspots in closely related sequenced genomes. Accessory tools facilitate design of hotspot-flanking primers for in silico and/or wet-science-based interrogation of cognate loci in unsequenced strains and analysis of islands for features suggestive of foreign origins; island-specific and genome-contextual features are tabulated and represented in schematic and graphical forms. To date we have used MobilomeFINDER to analyse several Enterobacteriaceae, Pseudomonas aeruginosa and Streptococcus suis genomes. MobilomeFINDER enables high-throughput island identification and characterization through increased exploitation of emerging sequence data and PCR-based profiling of unsequenced test strains; subsequent targeted yeast recombination-based capture permits full-length sequencing and detailed functional studies of novel genomic islands.
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影响因子：
7
作者：
Schwartz, S;Zhang, Z;Miller, W
通讯作者：
Miller, W
影响因子：
14.9
作者：
Ou HY;Smith R;Lucchini S;Hinton J;Chaudhuri RR;Pallen M;Barer MR;Rajakumar K
通讯作者：
Rajakumar K
影响因子：
2.9
作者：
Binnewies, Tim T.;Motro, Yair;Ussery, David W.
通讯作者：
Ussery, David W.
影响因子：
7
作者：
Schuler, GD
通讯作者：
Schuler, GD
影响因子：
5.8
作者：
Zhang, R;Zhang, CT
通讯作者：
Zhang, CT